Environmental Microbiology Reports最新文献

Bacteria on leaf surfaces encounter variable access to nutrients and water. This oligotrophic environment is partly due to cuticular waxes that render the leaf surface hydrophobic. While the alkane hydroxylase gene alkB is widespread in leaf-associated bacteria, its activity is not well defined. Here, we developed a bioreporter in Pseudomonas sp. FF2 (PFF2) to monitor alkB promoter activity in vitro and on Arabidopsis thaliana leaves. Single-cell analysis revealed a highly heterogeneous alkB promoter activity, with a subpopulation exhibiting strong fluorescence, consistent with alkane metabolism bet-hedging. On leaves, the promoter was active over the course of seven days, indicating constant access to alkanes over time. While our results support a potential role of alkB in bacterial adaptation to the phyllosphere, direct evidence of cuticular wax degradation is missing. Thus, future studies should trace the incorporation of plant-derived aliphatic compounds to elucidate the ecological relevance of alkB during leaf colonisation.

Anthropogenic activities may have profound impacts on the soil microbiome with consequences for soil health, agriculture and food production. Here, we investigated the impact of different fertilisation regimes on the composition of the bacterial soil microbiome in grassland ecosystems by 16S rRNA gene amplicon sequencing and in vitro growth experiments with culturable representatives of the bacterial core microbiota. We observed a large proportion of taxa shared across fertilisation regimes without significant differences in their evenness, but shifts in the composition of the bacterial core microbiome by fertilisation. These effects were most pronounced for fertilisation with pig slurry (PS). Analysis of microbiome multivariable association with linear models identified bacterial biomarker taxa for different fertilisation regimes. This enabled the selection of several culturable representatives for in vitro growth experiments. Consistent with the relative abundances of Bradyrhizobium, Nocardioides, and Solirubrobacter in field samples, the growth of Bradyrhizobium japonicum was inhibited by PS, while Nocardioides albus and Solirubrobacter pauli exhibited enhanced growth in its presence. Our results suggest that culturable representatives of the bacterial core soil microbiota can be identified and used to investigate the effects of specific parameters linked to anthropogenic impacts under controlled laboratory conditions.

Rivers are increasingly affected by human activities, leading to widespread eutrophication. However, the responses of riverine microbiomes to eutrophication remain poorly understood. In this study, we compared microbiomes between eutrophic urban rivers (UR) and relatively undisturbed natural rivers (NR) to elucidate how eutrophication influences community structures, assembly processes, functions and life-history strategies. Amplicon and metagenomic sequencing revealed that eutrophication substantially enhanced microbial abundance and diversity in riverine ecosystems, with UR harbouring a higher proportion of fast-growing, nitrogen-transforming and antibiotic-resistant taxa. Neutral and null model analyses further revealed that, while stochastic processes predominantly shaped communities in NR, deterministic environmental selection exerted stronger control under eutrophic conditions in UR. Correspondingly, microbial communities in UR exhibited higher 16S rRNA gene copy numbers (median 4.69 vs. 4.28), stronger codon usage bias (0.0209 vs. 0.0204), greater predicted growth rates (0.2664 vs. 0.1567 h⁻¹), larger genomes (5.91 vs. 5.19 Mb), higher guanine–cytosine content (57.68% vs. 56.41%) and enriched transposase genes (4.37% vs. 2.98%), collectively indicating a community-wide shift from K-selected to r-selected life-history strategies under eutrophication. Overall, this work elucidates how human activities reshape riverine microbial communities and life-history strategies, providing a basis for predicting the ecological outcomes of nutrient over-enrichment in fluvial environments.

Acute oak decline (AOD) is a rapidly progressing disease affecting various oak species (Quercus spp.). Recent studies have shown that AOD is associated with a consortium of Gram-negative, facultatively anaerobic bacteria (e.g., in Enterobacterales) in the United Kingdom and continental Europe. However, there is limited information on the bacterial contributions and key genera associated with oak diseases and broadleaf forest ecosystems in Nordic countries. The primary objective of this brief study was to collect the first data on the bark microbiomes of symptomatic, declining sessile oaks (Q. petraea) in Sweden. Pairs of healthy and diseased bark samples were collected from symptomatic trees near Ankarsrum (Kalmar County), Sweden. After total DNA extraction, the bacterial 16S rDNA region was amplified, and Oxford Nanopore Technologies was used for long-read high-throughput DNA metabarcoding of the bacterial microbiome. We found a dominance of enterobacterial phytopathogens, including two of the typical genera associated with AOD, Brenneria and Rahnella, exclusively in the diseased bark samples. Our findings extend the known distribution of AOD-associated bacteria to Sweden and Scandinavia and show that diseased oaks in this region host a microbiome similar to those found in other parts of Europe.

Biofilm formation is a phenomenon of great medical importance, also affecting food production. In the present work, we investigated the effect of the O-antigen length of lipopolysaccharide (LPS) of Salmonella Enteritidis on biofilm production and the physicochemical properties of Salmonella cells, using bacterial deletion mutants. We also analysed the influence of LPS O-antigen shortening on the composition of the outer membrane (OM) proteome of S. Enteritidis. We have shown that the shortening of the LPS O-antigen part is associated with decreased biofilm biomass formation in some mutants and that it also depends on the composition of the culture medium. Physicochemical properties of bacterial cells changed with the shortening of the O-antigen, promoting bacterial aggregation and influencing their hydrodynamic size, zeta potential, or hydrophobicity. We have also shown that shorter O-antigen alters the bacterial proteome in comparison to regular size O-antigen: flagellar FliC protein was down-regulated in most mutants, while the HptG as well as 50S ribosomal protein L7/L12 protein were up-regulated, suggesting increased protein synthesis activity. In some mutants, proteins involved in LPS biosynthesis were also upregulated: lipopolysaccharide core heptose(II)-phosphate phosphatase, acyl carrier protein, and undecaprenyl-phosphate alpha-N-acetylglucosaminyl 1-phosphate transferase, implying that the increased LPS biosynthesis is aimed at the replacement of the lacking LPS modal fractions in the S. Enteritidis mutants.

Seasonal flooding in Bangladesh poses severe public health risks through waterborne disease, yet a comprehensive, genomic-level understanding of the associated microbial hazards is lacking. This study presents a comprehensive shotgun metagenomic analysis of floodwaters from four districts of Bangladesh (Cumilla, Feni, Lakshmipur, and Noakhali) during the devastating 2024 floods, profiling the distribution of pathogenic bacteria, antimicrobial resistance genes, and virulence factors. A total of 12 samples were collected during peak flooding periods and processed using Illumina sequencing. Taxonomic profiling and resistome analysis were performed using MetaPhlAn4, ABRicate, and MEGAHIT, referencing the NCBI and CZ ID databases. Across all regions, 301 operational taxonomic units were identified. Feni exhibited the highest diversity of pathogenic species, including multidrug-resistant Klebsiella pneumoniae, toxigenic Pseudomonas aeruginosa, and mobilizable resistance plasmids (e.g., IncP1, Col440I). Noakhali samples revealed co-detection of zoonotic and emerging pathogens such as Aliarcobacter spp. and Streptococcus suis, along with key resistance genes like blaOXA and ermB. Microbial community clustering revealed strong spatial heterogeneity. This study provides genomic evidence that floodwaters harbour emerging pathogens and AMR. It strongly advocates for incorporating metagenomic tools into Bangladesh's national flood response and AMR monitoring frameworks.

While renowned for mitigating methane emissions via anaerobic oxidation of methane (AOM), the full ecological strategy of ANME-2a archaea still requires further exploration. This study looks beyond methane oxidation to map the protein landscape of ANME-2a, revealing an integrated system for metabolic autonomy and environmental resilience in this specific isolate. Using a feature-based protein network derived from 230 Methanosarcinales genomes, we uncovered a sophisticated modular architecture. Key findings demonstrate that the AOM machinery is not isolated but functionally coupled with distinct modules dedicated to auxiliary functions. Our analysis not only confirms that this ANME-2a isolate possesses the complete genomic toolkit for autonomous diazotrophy but also reveals the molecular blueprint for its integration with AOM. We show how key machinery has been specialised to support the organism's core energy metabolism, with its core nitrogenase components co-clustered within the same functional module as AOM electron transfer proteins. Furthermore, we identified a specialised module dedicated to ‘membrane fortification’ through the significant enrichment of pathways for archaeal lipid biosynthesis. This modular blueprint, which integrates core energy metabolism with nitrogen fixation and structural lipid production, provides a model for how diazotrophic ANME-2a lineages may thrive as robust, self-sufficient organisms adapted to dynamic, resource-limited ecosystems.

Recent studies show that Chlorella vulgaris, due to its richness in nutrients, exhibits protective properties for probiotic strains of lactic acid bacteria (LAB). This creates an opportunity to produce more effective probiotics. This study aimed to evaluate the effect of two supplements of C. vulgaris on the growth and survival of LAB exposed to adverse stress factors (pH = 3, the presence of 0.2% and 0.5% bile salts). Survival was evaluated after 0 and 6 h of culture in the adverse stress environment. The results obtained, indicated statistically significant (p < 0.05) differences in the obtained growth and survival of the tested groups of LAB in the presence of C. vulgaris and the control sample. The study found that LAB showed the lowest survival rate in the presence of 0.5% bile salts, regardless of the culture variant. The results obtained suggest that the effect of C. vulgaris on the growth and survival of LAB strains depends on various factors, including the culture environment, the source of isolation of the strain and the chemical composition and nutritional content of the preparation. The results confirm the protective nature of C. vulgaris in the presence of high concentrations of bile salts and low pH.

The green macroalga Ulva demonstrates exceptional growth rates, robustness, adaptability and potential for nitrogen and phosphorus removal; thus, it is a promising candidate for wastewater treatment and bioremediation. However, micropollutants in wastewater pose a potential threat to the holobiont. We explored the effects of emerging contaminants found in groundwater and wastewater on the microbiome of the cultivar Ulva compressa (conspecific with Ulva mutabilis). We identified the core microbiome by comparing the microbiome of the long-term cultivar (cultivated under laboratory conditions for over 70 years) with the native microbiome of U. compressa. Long-term cultivation was found to homogenise and reduce microbiome diversity; however, key functional taxa, including algal growth and morphogenesis-promoting bacteria, persisted. We subsequently challenged the core microbiome of the U. compressa cultivar with four antibiotics (chloramphenicol, erythromycin, oxytetracycline and sulfamethoxazole), two herbicides (atrazine, glyphosate) and three endocrine disruptors (bisphenol A, estradiol and ethinylestradiol). The micropollutants exerted distinct impacts, with antibiotics showing stronger effects than hormonal disruptors, which Ulva rapidly removes from the culture medium. In contrast, the microbiome did not contribute to the removal of these substances. These results indicate that although Ulva's microbiome is sensitive to environmental change, key functions with positive implications for aquaculture and ecosystem management are retained.

Our study aims to identify electrogenic bacteria and optimise culture conditions using different commercial and agro-industrial wastes as a sole carbon source. Potential candidates of electrogenic bacteria isolates (EBIs) were screened from anode-developed biofilm in a double-chambered microbial fuel cell (MFC) bioreactor system. Characterisation using cyclic voltammetry (CV) showed that the isolated bacteria had a potential bio-electrochemical property. Statistical techniques were used, including response surface methodology (RSM) with a central composite design (CCD). The highest cell growth, measured by optical density at 600 nm (OD_600nm) (1.1407 ± 0.00316) and cell dry weight (CDW) (0.02135 ± 0.00152 g/L), was obtained when commercial carbon glucose was used. Cost-effective, barley bran formulated media resulted in maximum growth, OD_600nm 1.52167 ± 0.03476 and CDW with 0.01541 ± 0.000071 g/L. The RSM optimised condition achieved a 32.3% fold increase of cell growth yield (OD_600nm) compared to unoptimised conditions. This is the first study to use 16S rRNA gene sequencing from anode biofilm to identify native Enterobacter species. In conclusion, the recently discovered isolate exhibited growth conditions between 18°C and 52°C, pH 3 and pH 11, and resistance to high salt concentrations (0.332 M NaCl). It might therefore be considered a potentially versatile biocatalyst candidate for MFC applications.